scholarly journals Defying Muller’s Ratchet: Ancient Heritable Endobacteria Escape Extinction through Retention of Recombination and Genome Plasticity

mBio ◽  
2016 ◽  
Vol 7 (3) ◽  
Author(s):  
Mizue Naito ◽  
Teresa E. Pawlowska
Keyword(s):  
Mycorrhizal Fungi ◽  
Arbuscular Mycorrhizal ◽  
Genome Plasticity ◽  
Escape Extinction ◽  
Muller's Ratchet ◽  
Evolutionary Forces ◽  
Slightly Deleterious Mutations ◽  
Muller’S Ratchet ◽  
Asexual Populations ◽  
Host Generation

ABSTRACT   Heritable endobacteria, which are transmitted from one host generation to the next, are subjected to evolutionary forces that are different from those experienced by free-living bacteria. In particular, they suffer consequences of Muller’s ratchet, a mechanism that leads to extinction of small asexual populations due to fixation of slightly deleterious mutations combined with the random loss of the most-fit genotypes, which cannot be recreated without recombination. Mycoplasma-related endobacteria (MRE) are heritable symbionts of fungi from two ancient lineages, Glomeromycota (arbuscular mycorrhizal fungi) and Mucoromycotina . Previous studies revealed that MRE maintain unusually diverse populations inside their hosts and may have been associated with fungi already in the early Paleozoic. Here we show that MRE are vulnerable to genomic degeneration and propose that they defy Muller’s ratchet thanks to retention of recombination and genome plasticity. We suggest that other endobacteria may be capable of raising similar defenses against Muller’s ratchet.

ADAPTIVE EVOLUTION OF ASEXUAL POPULATIONS UNDER MULLER'S RATCHET

Evolution ◽  
2004 ◽  
Vol 58 (7) ◽  
pp. 1403 ◽  
Author(s):  
Doris Bachtrog ◽  
Isabel Gordo
Keyword(s):  
Adaptive Evolution ◽  
Muller's Ratchet ◽  
Muller’S Ratchet ◽  
Asexual Populations

scholarly journals The advance of Muller's ratchet in a haploid asexual population: approximate solutions based on diffusion theory

1993 ◽  
Vol 61 (3) ◽  
pp. 225-231 ◽  
Author(s):  
Wolfgang Stephan ◽  
Lin Chao ◽  
Joanne Guna Smale
Keyword(s):  
Diffusion Theory ◽  
Large Population ◽  
Approximate Solutions ◽  
Diffusion Approximations ◽  
Asexual Population ◽  
Muller's Ratchet ◽  
Expected Time ◽  
Equilibrium Size ◽  
Muller’S Ratchet ◽  
Asexual Populations

SummaryAsexual populations experiencing random genetic drift can accumulate an increasing number of deleterious mutations, a process called Muller's ratchet. We present here diffusion approximations for the rate at which Muller's ratchet advances in asexual haploid populations. The most important parameter of this process is n0 = N e−U/s, where N is population size, U the genomic mutation rate and s the selection coefficient. In a very large population, n0 is the equilibrium size of the mutation-free class. We examined the case n0 > 1 and developed one approximation for intermediate values of N and s and one for large values of N and s. For intermediate values, the expected time at which the ratchet advances increases linearly with n0. For large values, the time increases in a more or less exponential fashion with n0. In addition to n0, s is also an important determinant of the speed of the ratchet. If N and s are intermediate and n0 is fixed, we find that increasing s accelerates the ratchet. In contrast, for a given n0, but large N and s, increasing s slows the ratchet. Except when s is small, results based on our approximations fit well those from computer simulations.

scholarly journals Muller’s Ratchet in Asexual Populations Doomed to Extinction

2018 ◽  
Author(s):  
Logan Chipkin ◽  
Peter Olofsson ◽  
Ryan C. Daileda ◽  
Ricardo B. R. Azevedo
Keyword(s):  
Process Model ◽  
Population Decline ◽  
Extinction Time ◽  
Deleterious Mutations ◽  
Multitype Branching Process ◽  
Muller's Ratchet ◽  
Constant Size ◽  
Muller’S Ratchet ◽  
Asexual Populations ◽  
Mutational Meltdown

AbstractAsexual populations are expected to accumulate deleterious mutations through a process known as Muller’s Ratchet. Lynch, Gabriel, and colleagues have proposed that the Ratchet eventually results in a vicious cycle of mutation accumulation and population decline that drives populations to extinction. They called this phenomenon mutational meltdown. Here, we analyze the meltdown using a multitype branching process model where, in the presence of mutation, populations are doomed to extinction. We find that extinction occurs more quickly in small populations, experiencing a high deleterious mutation rate, and mutations with more severe deleterious effects. The effects of mutational parameters on extinction time in doomed populations differ from those on the severity of Muller’s Ratchet in populations of constant size. We also 1nd that mutational meltdown, although it does occur in our model, does not determine extinction time. Rather, extinction time is determined by the expected impact of deleterious mutations on fitness.

scholarly journals Integrating ecology and evolution to study hypothetical dynamics of algal blooms and Muller’s ratchet using Evolvix

2017 ◽  
Author(s):  
Sarah Northey ◽  
Courtney Hove ◽  
Justine Kao ◽  
Jon Ide ◽  
Janel McKinney ◽  
...  
Keyword(s):  
Dna Repair ◽  
Nutrient Availability ◽  
Continuous Time ◽  
Algal Blooms ◽  
Predation Pressure ◽  
Mutation Rates ◽  
Deleterious Mutations ◽  
Muller's Ratchet ◽  
Slightly Deleterious Mutations ◽  
Muller’S Ratchet

Algal blooms have been the subject of considerable research as they occur over various spatial and temporal scales and can produce toxins that disrupt their ecosystem. Algal blooms are often governed by nutrient availability however other limitations exist. Algae are primary producers and therefore subject to predation which can keep populations below levels supported by nutrient availability. If algae as prey mutate to gain the ability to produce toxins deterring predators, they may increase their survival rates and form blooms unless other factors counter their effective increase in growth rate. Where might such mutations come from? Clearly, large populations of algae will repeatedly experience mutations knocking-out DNA repair genes, increasing mutation rates, and with them the chance of acquiring de-novo mutations producing a toxin against predators. We investigate this hypothetical scenario by simulation in the Evolvix modeling language. We modeled a sequence of steps that in principle can allow a typical asexual algal population to escape predation pressure and form a bloom with the help of mutators. We then turn our attention to the unavoidable side effect of generally increased mutation rates, many slightly deleterious mutations. If these accumulate at sufficient speed, their combined impact on fitness might place upper limits on the duration of algal blooms. These steps are required: (1) Random mutations result in the loss of DNA repair mechanisms. (2) Increased mutation rates make it more likely to acquire the ability to produce toxins by altering metabolism. (3) Toxins deter predators providing algae with growth advantages that can mask linked slightly deleterious mutational effects. (4) Reduced predation pressure enables blooms if algae have sufficient nutrients. (5) Lack of recombination results in the accumulation of slightly deleterious mutations as predicted by Muller’s ratchet. (6) If fast enough, deleterious mutation accumulation eventually leads to mutational meltdown of toxic blooming algae. (7) Non-mutator algal populations are not affected due to ongoing predation pressure. Our simulation models integrate ecological continuous-time dynamics of predator-prey systems with the population genetics of a simplified Muller’s ratchet model using Evolvix. Evolvix maps these models to Continuous-Time Markov Chain models that can be simulated deterministically or stochastically depending on the question. The current model is incomplete; we plan to investigate many parameter combinations to produce a more robust model ensemble with stable links to reasonable parameter estimates. However, our model already has several intriguing features that may allow for the eventual development of observation methods for monitoring ecosystem health. Our work also highlights a growing need to simulate integrated models combining ecological processes, multi-level population dynamics, and evolutionary genetics in a single computational run.

scholarly journals Integrating ecology and evolution to study hypothetical dynamics of algal blooms and Muller’s ratchet using Evolvix

2017 ◽  
Author(s):  
Sarah Northey ◽  
Courtney Hove ◽  
Justine Kao ◽  
Jon Ide ◽  
Janel McKinney ◽  
...  
Keyword(s):  
Dna Repair ◽  
Nutrient Availability ◽  
Continuous Time ◽  
Algal Blooms ◽  
Predation Pressure ◽  
Mutation Rates ◽  
Deleterious Mutations ◽  
Muller's Ratchet ◽  
Slightly Deleterious Mutations ◽  
Muller’S Ratchet

Algal blooms have been the subject of considerable research as they occur over various spatial and temporal scales and can produce toxins that disrupt their ecosystem. Algal blooms are often governed by nutrient availability however other limitations exist. Algae are primary producers and therefore subject to predation which can keep populations below levels supported by nutrient availability. If algae as prey mutate to gain the ability to produce toxins deterring predators, they may increase their survival rates and form blooms unless other factors counter their effective increase in growth rate. Where might such mutations come from? Clearly, large populations of algae will repeatedly experience mutations knocking-out DNA repair genes, increasing mutation rates, and with them the chance of acquiring de-novo mutations producing a toxin against predators. We investigate this hypothetical scenario by simulation in the Evolvix modeling language. We modeled a sequence of steps that in principle can allow a typical asexual algal population to escape predation pressure and form a bloom with the help of mutators. We then turn our attention to the unavoidable side effect of generally increased mutation rates, many slightly deleterious mutations. If these accumulate at sufficient speed, their combined impact on fitness might place upper limits on the duration of algal blooms. These steps are required: (1) Random mutations result in the loss of DNA repair mechanisms. (2) Increased mutation rates make it more likely to acquire the ability to produce toxins by altering metabolism. (3) Toxins deter predators providing algae with growth advantages that can mask linked slightly deleterious mutational effects. (4) Reduced predation pressure enables blooms if algae have sufficient nutrients. (5) Lack of recombination results in the accumulation of slightly deleterious mutations as predicted by Muller’s ratchet. (6) If fast enough, deleterious mutation accumulation eventually leads to mutational meltdown of toxic blooming algae. (7) Non-mutator algal populations are not affected due to ongoing predation pressure. Our simulation models integrate ecological continuous-time dynamics of predator-prey systems with the population genetics of a simplified Muller’s ratchet model using Evolvix. Evolvix maps these models to Continuous-Time Markov Chain models that can be simulated deterministically or stochastically depending on the question. The current model is incomplete; we plan to investigate many parameter combinations to produce a more robust model ensemble with stable links to reasonable parameter estimates. However, our model already has several intriguing features that may allow for the eventual development of observation methods for monitoring ecosystem health. Our work also highlights a growing need to simulate integrated models combining ecological processes, multi-level population dynamics, and evolutionary genetics in a single computational run.

scholarly journals Does Muller's ratchet work with selfing?

1978 ◽  
Vol 32 (3) ◽  
pp. 289-293 ◽  
Author(s):  
R. Heller ◽  
J. Maynard Smith
Keyword(s):  
Large Class ◽  
Deleterious Mutations ◽  
Asexual Population ◽  
Muller's Ratchet ◽  
Slightly Deleterious Mutations ◽  
Muller’S Ratchet

SUMMARYThe accumulation of deleterious mutations in a finite diploid selfing population is investigated. It is shown that the conditions for accumulation are very similar to those for the accumulation of mutations in an asexual population by ‘Muller's ratchet’. The ratchet is likely to operate in both types of population if there is a large class of slightly deleterious mutations.

scholarly journals The constraints of finite size in asexual populations and the rate of the ratchet

1995 ◽  
Vol 66 (3) ◽  
pp. 241-253 ◽  
Author(s):  
Damian D. G. Gessler
Keyword(s):  
Negative Binomial ◽  
Finite Size ◽  
Mutation Accumulation ◽  
Necessary Condition ◽  
Mutation Pressure ◽  
Actual Distribution ◽  
Muller's Ratchet ◽  
State Strength ◽  
Muller’S Ratchet ◽  
Asexual Populations

SummaryAn analysis of mutation accumulation in finite, asexual populations shows that by modeling discrete individuals, a necessary condition for mutation–selection balance is often not met. It is found that over a wide parameter range (whenever N e−μ/s < 1, where N is the population size, μ is the genome-wide mutation rate, and s is the realized strength of selection), asexual populations will fail to achieve mutation–selection balance. This is specifically because the steady-state strength of selection on the best individuals is too weak to counter mutation pressure. The discrete nature of individuals means that if the equilibrium level of mutation and selection is such that less than one individual is expected in a class, then equilibration towards this level acts to remove the class. When applied to the classes with the fewest mutations, this drives mutation accumulation. This drive is in addition to the well-known identification of the stochastic loss of the best class as a mechanism for Muller's ratchet. Quantification of this process explains why the distribution of the number of mutations per individual can be markedly hypodispersed compared to the Poisson expectation. The actual distribution, when corrected for stochasticity between the best class and the mean, is akin to a shifted negative binomial. The parameterization of the distribution allows for an approximation for the rate of Muller's ratchet when N e−μ/s < 1. The analysis is extended to the case of variable selection coefficients where incoming mutations assume a distribution of deleterious effects. Under this condition, asexual populations accumulate mutations faster, yet may be able to survive longer, than previously estimated.

Temporal dynamics of mycorrhizal fungal communities and co-associations with grassland plant communities following experimental manipulation of rainfall

2019 ◽  
Author(s):  
Coline Deveautour ◽  
Sally Power ◽  
Kirk Barnett ◽  
Raul Ochoa-Hueso ◽  
Suzanne Donn ◽  
...  
Keyword(s):  
Community Composition ◽  
Plant Community ◽  
Plant Communities ◽  
Fungal Community ◽  
Mycorrhizal Fungi ◽  
Temporal Dynamics ◽  
Arbuscular Mycorrhizal ◽  
Fungal Communities ◽  
Plant Responses ◽  
Rainfall Regimes

Climate models project overall a reduction in rainfall amounts and shifts in the timing of rainfall events in mid-latitudes and sub-tropical dry regions, which threatens the productivity and diversity of grasslands. Arbuscular mycorrhizal fungi may help plants to cope with expected changes but may also be impacted by changing rainfall, either via the direct effects of low soil moisture on survival and function or indirectly via changes in the plant community. In an Australian mesic grassland (former pasture) system, we characterised plant and arbuscular mycorrhizal (AM) fungal communities every six months for nearly four years to two altered rainfall regimes: i) ambient, ii) rainfall reduced by 50% relative to ambient over the entire year and iii) total summer rainfall exclusion. Using Illumina sequencing, we assessed the response of AM fungal communities sampled from contrasting rainfall treatments and evaluated whether variation in AM fungal communities was associated with variation in plant community richness and composition. We found that rainfall reduction influenced the fungal communities, with the nature of the response depending on the type of manipulation, but that consistent results were only observed after more than two years of rainfall manipulation. We observed significant co-associations between plant and AM fungal communities on multiple dates. Predictive co-correspondence analyses indicated more support for the hypothesis that fungal community composition influenced plant community composition than vice versa. However, we found no evidence that altered rainfall regimes were leading to distinct co-associations between plants and AM fungi. Overall, our results provide evidence that grassland plant communities are intricately tied to variation in AM fungal communities. However, in this system, plant responses to climate change may not be directly related to impacts of altered rainfall regimes on AM fungal communities. Our study shows that AM fungal communities respond to changes in rainfall but that this effect was not immediate. The AM fungal community may influence the composition of the plant community. However, our results suggest that plant responses to altered rainfall regimes at our site may not be resulting via changes in the AM fungal communities.

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